Saturday, January 31, 2015

Are Linnean ranks and cladism incompatible? (That special issue)

(The following is the eighth part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

The next contribution is that of the late Richard Brummitt who died between the Melbourne symposium promoting paraphyletic taxa and the publication of the resulting special issue. The manuscript was apparently adopted from a talk he gave at the symposium.

Brummitt's death was a great loss to the botanical community; he was influential, knowledgeable and had friends across the entire planet. In the present context, I respect him as the only proponent of paraphyletic taxa whose argumentation ever made sense to me – if, that is, certain controversial assumptions are accepted. This may sound like faint praise, but it is more than can be said about many other arguments that are used in the discussion.

Brummitt was also certainly a good writer, as will be evident in what follows, but nonetheless I find myself unable to agree with his conclusions. I will go through the paper from the beginning until we hit the crux of his case.

Tuesday, January 27, 2015

Botany picture #191: Scleranthus biflorus

Apparently I cannot currently muster the energy to deal with the next paper from that special issue, so here is another picture from the recent field trip. Scleranthus biflorus (Caryophyllaceae), New South Wales, 2015. More weird than pretty, I'll admit. The spiky balls to the left and in the background are fruiting heads of Acaena novae-zeelandiae (Rosaceae).

Saturday, January 24, 2015

Au contraire

One of the things that has often struck me when contemplating religion is that I do not only disagree with several core claims made in its favour, but I feel that these claims are completely upside-down. In other words, not only are they wrong, but instead I feel that they are so much the opposite of what is really the case that one might start to suspect psychological projection to be at work.

I am not thinking of claims about actual evidence for the truth of religion - that is a different issue - but of second order claims about the benefits of religion. In particular, popular pronouncements along these lines:
  1. Life without god is totally pointless and meaningless; we need god and divine commands to give meaning to our lives.
  2. The conclusion that we are annihilated at death is depressing, and belief in an immortal soul, in our continued existence after death is much better.
  3. Atheists must be immoral because without gods and holy books they have nothing to base their morals on. Therefore, they should not be trusted.
One after the other...

Tuesday, January 20, 2015

Botany picture #190: Coreopsis lanceolata

One of the amazing things about daisies (Asteraceae) that is hidden to many non-botanists is how they do a lot of things with an inflorescence that other plants do with a solitary flower. To me this appears to be a clear case of convergent evolution: There is a limited number of good solutions to a given problem, and so evolution converges on them over and over again.

As background, most readers will know that what appears to be a daisy "flower" is really a head consisting of numerous small flowers called florets:

The small structures in the middle are the disc florets, some of them in bud, some of them open, and the latter each with five petals and a ring of fused stamens surrounding a forked style in the middle. But, unbelievable as it may sound, the large yellow pseudo-petals around the flower head are also individual flowers. They are called ray florets and are essentially an extreme version of a zygomorphic flower like those found in Goodenias or Lobelias, for example; in this case, the three petals forming the lower lip of the flower are massive enlarged while the two petals forming the upper lip are reduced. In many species they also have their own style (although no stamens), further demonstrating their true nature.

Now as I wrote above, daisy heads sometimes converge on the same functionality as individual flowers of other plant groups. The case I noticed recently is Coreopsis lanceolata. This species, introduced to Australia from North America, has differentiated bracts. The outermost "pretend" to be a calyx, so they have the same role as the outermost, small, green leaf organs of a regular solitary flower and, it has to be said, as the bracts of most other daisies: to protect the developing organ in bud.

However, in Coreopsis lanceolata there is also an inner group of bracts that are larger and less herbaceous, often already brownish when the head is in flower:

What those inner bracts are good for becomes apparent when the head has finished flowering. The petaloid ray florets fall off, each disc floret starts forming one one-seeded fruit, and at the same time the inner bracts close around the developing fruits to protect them:

When the fruits are fully developed, the inner bracts spread apart again to allow their release. In this way, these bracts behave pretty much like the carpels forming a capsule in many solitary flowers.

Don't know about you, but I find this pretty amazing.

Saturday, January 17, 2015

Botany picture #189: Senecio pinnatifolius

The past few days I was on a field trip to Kosciuszko National Park with one colleague and two students, and I came back totally tired. I think twelve years ago running around at ca. 2,000 metres above sea level was less exhausting for me.

I don't need to write much about the area because I already did so, after I undertook a similar field trip two years ago: first part, second part. So this time around let's simply combine a mountain landscape with a botany picture: Senecio pinnatifolius var. pleiocephalus (Asteraceae) on the way from Charlotte Pass to Blue Lake. Daisies are an extremely important part of the alpine flora of this country, perhaps even more so than on other continents.

Monday, January 12, 2015

Much ado about absent ancestors

(The following is the seventh part of a series of posts on an Annals of the Missouri Botanical Garden special issue on “Evolutionary Systematics and Paraphyly”. All posts in this series are tagged with “that special issue”.)

Pages 79 to 88 of this special issue meant to promote the acceptance of supraspecific paraphyletic taxa in biological classifications are taken up by a contribution entitled Paraphyly and polyphyly in the worldwide tribe Rubieae (Rubiaceae): Challenges for generic delimitation. Written by Friedrich Ehrendorfer, Michael Barfuss and Vladimir Vladimirov, it is perhaps best described as a concise review article summarising the current state of knowledge about phylogenetic relationships in their group of interest, and as such I found it extremely interesting and rewarding to read.

Even if they are not familiar with the scientific name, most people in the northern hemisphere will know Rubieae. They are characteristic herbs with seemingly whorled leaves; only seemingly because in reality there are only two true leaves, and the additional members of each whorl are derived from stipules, as demonstrated by the fact that only up to two side branches arise from each node. The flowers of these plants are usually small, radiate and white or yellow. The group has an extremely wide distribution; there are even native representatives here in Australia.

The phylogenetic studies discussed in the paper show that the two largest genera that are traditionally accepted in the Rubieae, Galium and Asperula, are horribly non-monophyletic in their current circumscriptions. Faced with this situation and considering the context in which the paper has been published, one would now expect, or at least I would expect, that the authors argue for the continued acceptance of these genera as non-monophyletic. That was, after all, the whole point of the symposium in Vienna that inspired the special issue.

Friday, January 9, 2015

Comparison of phylogenetic tree viewing programs: TreeView, FigTree, Dendroscope

It seems as if I could productively conclude the theme of how to root phylogenetic trees by providing an overview of the tree viewers I have some experience with.

When you do a phylogenetic analysis in programs such as PAUP, TNT, RAxML, MrBayes or BEAST, you do get a phylogenetic tree, but it is not a graphic to look at. Instead, the standard format for phylogenetic trees is that of a text file in the Newick format, e.g. "(speciesA:4,(speciesB:6,(speciesC:2,speciesD:3)95:2)76:1)". The brackets show how the terminals of the tree are grouped, the numbers after the colons are branch lengths, and the other numbers following directly behind brackets are clade support values. All the information is there, but that is not a very clear way of displaying a tree, especially if it has dozens or hundreds of terminals.

The programs discussed below are used to display phylogenetic trees and to transform them into vector graphic files that can be used for the preparation of scientific publications.

The screen shots below show the same tree displayed in each program as a phylogram with clade support values.